Civet Dependencies
civet runs on MacOS and Linux. The conda environment recipe may not build on Windows (I haven't tested it), but can be run using the Windows subsystem for Linux.
To run civet, you will need
- Conda version 4.9 or greater, we use Miniconda3.. Can be downloaded from here
- Access to a set of background data files, minimally a metadata csv file and an aligned fasta file. More information about this data here
Dependencies
- biopython
- iqtree>=2.1
- minimap2>=2.17
- python=3.9
- snakemake-minimal<=6.8.0
- cov-ert::jclusterfunk>=0.0.25
- gofasta==0.0.5
- mako>=1.1
- snipit
- https://github.com/cov-lineages/scorpio.git
- https://github.com/cov-lineages/constellations.git